Stress early in life puts the individual at a greater risk for developing mental disorders in adulthood. The animal model of maternal separation involves daily removal of pups from their mother over the early postnatal period and leads to several behavioral deficits in adults. Since this period corresponds to a time of extensive developmental changes in the glutamatergic system, glutamate receptor mRNA expression was studied in the hippocampus and prefrontal cortex. Male Wistar rats were either separated from their mother for 15 min (MS15 or 'handling') or 360 min (MS360) once a day from pnd 1-21 and glutamate receptor expression levels were measured at 25 weeks of age using real-time RT-PCR analysis. A third group of animal facility reared (AFR) rats was included as a control for the handling group. In the hippocampus, mRNA expression of NMDA NR2B and AMPA GluR1 and GluR2 receptors was significantly lower in MS360 rats relative to MS15. In addition, expression of the glutamate transporter GLAST was increased in MS360 relative to MS15. No differences were observed for AFR rats relative to MS15, which indicates that the hippocampal effects were not a result of handling or maternal care. For the prefrontal cortex, no difference in mRNA expression was observed for NMDA NR2A and NR2B or AMPA GluR1 and GluR2. These findings suggest that prolonged maternal separation produces neuroadaptive changes in the hippocampus that may, at least partially, account for the behavioral deficits previously observed in this animal model.